file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 39.00 41.00 43.00 42.52 44.00 45.00
## [1] 40
## [1] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42 42 42 42 43 43 43 43 43 43 43
## [26] 43 43 43 43 44 44 44 44 44 44 44 44 45 45 45
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
##
## FALSE TRUE
## 1643 357
##
## FALSE TRUE <NA>
## 21 1622 357
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 6900 0.118699020 90.14412
## 2: gene 161 0.002485395 99.77003
## total_counts
## 1: 8310
## 2: 174
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00857 90.44551 99.20296 90.72478 99.93429 100.00000
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 60.04 81.87 72.81 92.88 97.99
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: A2M A2M A2M ENSG00000175899 FALSE
## 2: A2ML1-AS1 A2ML1-AS1 A2ML1-AS1 ENSG00000256661 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 5826 0.1207987
## 2: NCBITaxon:9606 gene 11030 0.2138297
## pct_dropout_by_counts total_counts selected
## 1: 91.67821 8457 1
## 2: 84.24488 14970 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MYO16" "PPEF1" "EPB41L4B" "SCD" "GALNT16" "FRK"
## [7] "SIPA1L2" "APOC1" "EPSTI1" "C4orf45" "EPHX4" "SSR4"
## [13] "ARHGAP8" "CCDC124" "DCN" "ABCA7" "ATP2B3" "PPP1R15A"
## [19] "CASS4" "SLC7A5" "RELB" "ISYNA1" "ADAP1" "EPHB6"
## [25] "UNC5B" "ARID3A" "DUSP1" "PMEPA1" "ANXA1" "HAVCR2"
## [31] "MICAL1" "MVB12A" "SH3GL1" "SLC43A1" "CNKSR3" "FBXO32"
## [37] "PDPN" "ITGA2" "PIK3CD" "MYO1D" "MB21D2" "TMEM229B"
## [43] "HAUS7"
## [1] 2
## [1] "AHRR" "SLC26A8" "WDR64" "FILIP1L"
## [5] "GLIPR1L1" "AP000233.4" "RP1-15D23.2" "TMLHE-AS1"
## [9] "RP11-547I7.1" "ST7-AS2" "AC017101.10" "ASTN2-AS1"
## [13] "CCDC192" "RP11-417B4.2" "RP11-46O21.2" "GRM3-AS1"
## [17] "AC037445.1" "RP11-666F17.1" "RP11-109I13.2" "LINC02250"
## [21] "LINC01695" "LINC01829" "GS1-433O24.1" "AC008067.2"
## [25] "LINC02877" "RP11-657O9.1" "RP5-1101C3.1" "GK-AS1"
## [29] "RP11-115N4.1" "RP11-274H2.2" "RP11-223C24.1" "RP11-120A1.1"
## [33] "RP11-39E3.3" "CTD-3239E11.2" "RP11-463D19.1" "RP11-1H15.2"
## [37] "A2ML1-AS1" "RP11-887P2.5" "DIO2-AS1" "CRIM1-DT"
## [41] "RP11-58G13.1" "CH17-140K24.2" "RP11-313M3.2" "RP11-394G3.3"
## [45] "RP11-555K12.4"
## [1] 3
## [1] "SEL1L2" "POLR2I" "H3-3B" "CA1"
## [5] "AGBL3" "MEGF11" "BTG2" "SHOC1"
## [9] "MFSD4B" "SGCZ" "MT1X" "HES4"
## [13] "RP1-292B18.4" "RP11-131L23.1" "MRPS9-AS2" "SNAP25-AS1"
## [17] "GNA14-AS1" "RP1-232L24.3" "AC009501.4" "GNG12-AS1"
## [21] "LINC00513" "RBMS3-AS3" "ZBTB20-AS5" "PRKAR2B-AS1"
## [25] "RORA-AS1" "LINC01618" "RP11-157I4.4" "RP11-452H21.1"
## [29] "MPPED2-AS1" "AP000487.6" "CTD-2537O9.1" "LINC02740"
## [33] "LINC02745" "RP11-144F15.1" "LINC02327" "RP11-363J20.2"
## [37] "RP11-524F11.2" "CTC-513N18.6" "ARRDC3-AS1" "RP11-470M1.2"
## [41] "BCL6-AS1" "CTD-2313D3.2" "RP11-592G13.2" "RP11-341N18.1"
## [1] 4
## [1] "WSCD2" "SRPX2" "TENT5A" "DNAH6"
## [5] "PKIB" "HS3ST3A1" "SAXO1" "SCN11A"
## [9] "FSTL5" "RNF212" "CLDN4" "RFX8"
## [13] "NPSR1-AS1" "COL5A2" "MT1H" "RP11-306O13.1"
## [17] "AC007277.3" "RNF212B" "RP11-344B5.2" "RP11-735G4.1"
## [21] "LINC01036" "AC009264.1" "LINC01934" "LINC01376"
## [25] "RP11-624M8.1" "PTPRG-AS1" "RP11-167H9.4" "LINC02355"
## [29] "RP11-436F23.1" "ZFHX4-AS1" "C8orf37-AS1" "RP11-124B13.1"
## [33] "RP11-511B23.2" "PRANCR" "RP11-260G13.1" "LINC01572"
## [37] "RP11-397A16.1" "AC005786.7" "LINC00907" "RP11-290O12.2"
## [41] "RP11-69G16.2" "RP4-681L3.3" "RP11-725F23.1" "RP11-314E10.1"
## [1] 5
## [1] "MT1G" "MTERF1" "TMEM241" "RERG"
## [5] "MT1E" "DLEU1" "LINC01006" "HDHD5-AS1"
## [9] "CC2D2B" "LEKR1" "DIO2" "HEPN1"
## [13] "PLCG1-AS1" "SOX21-AS1" "HDAC2-AS2" "LINC01344"
## [17] "RP4-613B23.1" "RP1-45C12.1" "LINC01937" "RP11-142A5.1"
## [21] "AC079305.11" "LINC02652" "PKN2-AS1" "H2AZ1-DT"
## [25] "MEF2C-AS2" "LINC02234" "HS3ST5" "LINC01340"
## [29] "LINC01950" "RP11-404I7.2" "LIX1-AS1" "RP1-84O15.2"
## [33] "LINC00534" "RP11-804N13.1" "RP11-431M3.1" "RP11-526N18.1"
## [37] "RP11-242P2.1" "LINC00637" "RP11-103J8.1" "LINC00540"
## [41] "LINC01727" "RP11-589M4.5" "RP3-383B8.1" "RP11-346I3.7"
## [45] "RP11-399K19.1"
## [1] 6
## [1] "ARHGAP44" "SNCAIP" "MROH8" "PUDP"
## [5] "KCTD1" "FADS2" "EFCAB11" "SLC14A1"
## [9] "TEX9" "MAP3K7CL" "STPG2" "LMOD1"
## [13] "RFLNA" "ADAP2" "SLC24A3" "ADD3-AS1"
## [17] "LIPE-AS1" "COL28A1" "LINC00571" "LMCD1-AS1"
## [21] "AC097721.2" "RP11-498J9.2" "LINC02884" "RAP2C-AS1"
## [25] "RP11-120D5.1" "RPL34-DT" "LINC00886" "SUCLG2-AS1"
## [29] "RP11-461O7.1" "RP11-11N9.4" "RP11-130F10.1" "RP11-284M14.1"
## [33] "RP11-582J16.4" "RP11-20I20.2" "RP11-727A23.10" "SPESP1"
## [37] "RP11-739G5.1" "PLS3-AS1" "SYNPO2L-AS1" "RP1-84D21.2"
## [41] "RNF19A" "NOL4L" "ZNF358"
## [1] 7
## [1] "DNAH9" "BID" "GAB2" "FAM107B" "SGK2" "PLS3"
## [7] "SLC39A14" "SLC2A9" "PPM1H" "EEPD1" "MASP1" "PRR5L"
## [13] "LPAR4" "PTH1R" "CA3" "CERS6" "NIPAL3" "MAP3K9"
## [19] "HDAC9" "MAST3" "SH3PXD2A" "IL1R1" "ASL" "ZFP36"
## [25] "IRAK2" "NAV1" "KIAA0513" "EGF" "MAGI1" "DEPTOR"
## [31] "MYO1E" "TMEM200A" "IKBIP" "SPSB1" "MOB3A" "PAWR"
## [37] "OSTN" "AFAP1" "MEF2B" "CPEB1"
## [1] 8
## [1] "RP11-793A3.2" "BAIAP3" "TESC" "DNAH11"
## [5] "USP9Y" "LRAT" "HELB" "SCN1A"
## [9] "CCDC175" "ANGPT1" "SAMD3" "ADCY1"
## [13] "NLGN4Y" "SLITRK5" "NPNT" "TTTY14"
## [17] "CAVIN1" "PLCXD3" "CHST6" "UTY"
## [21] "SAMD11" "OVCH1" "LAMA2" "S1PR3"
## [25] "AP001347.6" "TTTY10" "RP11-469A15.2" "LINC00278"
## [29] "RP1-187B23.1" "RP11-146I2.1" "IQCM" "RP11-305L7.3"
## [33] "CTD-2643I7.5" "RP11-190P13.2" "RTL9" "KCNK15-AS1"
## [37] "RP11-259K15.2" "RP11-876N24.2" "RP11-60A24.3" "MAFG-DT"
## [41] "MIR23AHG" "RP11-403A3.2" "RP3-365E2.1"
## [1] 9
## [1] "CD38" "HHAT" "ANKRD7" "PAPPA2"
## [5] "TFAP2E" "PLAGL1" "RGS22" "PEBP4"
## [9] "LIX1" "CHODL" "PKD1L1" "KIF6"
## [13] "FREM1" "ALDH1A1" "PRTG" "VWA3B"
## [17] "ODAD2" "WDR97" "ENO4" "SCOC-AS1"
## [21] "MAMDC2-AS1" "CHL1-AS2" "LINC01876" "RP11-162D16.2"
## [25] "RP1-167A14.2" "LINC01515" "ZRANB2-AS2" "RP11-195C7.1"
## [29] "RP11-132E11.2" "LINC01358" "CDKN2B-AS1" "RP11-1252I4.2"
## [33] "RP4-785G19.5" "LINC00958" "CTC-347C20.1" "CTB-178M22.2"
## [37] "RP11-708B6.2" "LINC02320" "RP11-16B13.1" "CRTC3-AS1"
## [41] "RP11-525K10.3" "RP11-396B14.2" "LINC00506" "RP11-175O15.1"
## [1] 10
## [1] "USH1C" "DPYSL3" "UBE3D" "COL4A2"
## [5] "MIPOL1" "STOX2" "GPC6" "HMGN5"
## [9] "AC105760.2" "RP11-550I24.2" "MALAT1" "RP11-352M15.1"
## [13] "RARB" "SLCO1A2" "RFX2" "P2RX7"
## [17] "CDH20" "MYOM1" "FGL1" "PPARGC1A"
## [21] "LIN7A" "RFX4" "PRR12" "IQCA1"
## [25] "DMGDH" "CCDC146" "DPYSL5" "TCAP"
## [29] "FIGN" "TSHZ2" "FAM174B" "TSBP1-AS1"
## [33] "RP11-69I8.3" "RP11-348F1.3" "LINC00342" "MIR4300HG"
## [37] "RP11-279O9.4" "TAPT1-AS1" "SPANXA2-OT1" "RP11-799O21.2"
## [41] "RP11-125C10.1"
## [1] 11
## [1] "CLIC5" "PDE8B" "ACAT2" "HS3ST3B1" "HESX1"
## [6] "AF131217.1" "AQP1" "LRRC24" "GTF2IRD1" "ATP9A"
## [11] "ITPKC" "PIR" "EBF4" "CERS4" "PLIN3"
## [16] "ABCC3" "ST8SIA1" "ZC4H2" "ZBTB46" "GFAP"
## [21] "TMCC2" "CDR2" "SSH2" "FSIP1" "RHPN1"
## [26] "ARHGAP35" "ZER1" "SLC20A2" "PTPN9" "CLIC4"
## [31] "IFFO2" "NPAS2" "PFKFB3" "HAP1" "SLC35E3"
## [36] "SYNM" "CMTM4" "RILPL1" "LIME1" "FBXO17"
## [41] "ATP6V0D1-DT"
## [1] 12
## [1] "ANOS1" "RRAGD" "PSD" "ATP11A"
## [5] "MAOB" "ANKRD24" "KIAA1549L" "PHACTR2"
## [9] "TACR1" "ELL2" "MGAT3" "UNC13A"
## [13] "WARS1" "SLC44A3" "PRSS23" "BEND6"
## [17] "SPOCK1" "ANKRD33B" "METTL2B" "HOPX"
## [21] "PRELID2" "PCLO" "C9orf153" "IER5L"
## [25] "MAML3" "FBXO16" "CTA-292E10.6" "OSMR-AS1"
## [29] "TRMT9B" "IDH2-DT" "RP1-41C23.1" "RP11-125D12.3"
## [33] "CTD-2126E3.6" "KLF6" "P3H2" "COL5A1"
## [37] "TMTC1" "ZNF208" "ARHGEF3" "TPST1"
## [41] "RGS6" "TCEA3" "RP11-513I15.6" "PCAT1"
## [1] 13
## [1] "SPATA6L" "SLC16A6" "WNT5B" "PDE10A"
## [5] "GDAP1L1" "IFI44L" "FHAD1" "SLC22A3"
## [9] "DUSP15" "ERICH3" "CCBE1" "LGALSL-DT"
## [13] "TARID" "LINC01768" "RP1-223B1.1" "LINC00326"
## [17] "KIF5C-AS1" "LINC01503" "NPIPB2" "LINC00877"
## [21] "CXXC4-AS1" "BAALC-AS1" "C5orf17" "RP11-380P13.1"
## [25] "LINC00923" "RP11-745L13.2" "CENATAC-DT" "MTRNR2L8"
## [29] "MAP1LC3B2" "HIF1A-AS3" "RP11-798K3.2" "DISC1FP1"
## [33] "AC007193.6" "LINC01374" "RP11-496B10.6" "RP11-364P22.4"
## [37] "RP11-492O8.3" "CTD-2040G12.2" "AC006296.4" "RP11-520F22.1"
## [41] "RP11-215I16.3" "KRTAP5-AS1"
## [1] 14
## [1] "MOGAT1" "TMEM132B" "SYCP2L" "UNC5D"
## [5] "SGCD" "MACROD2" "OBI1-AS1" "RP11-154H17.1"
## [9] "MGAM" "RP11-111A21.1" "RP11-571L19.7" "CTD-2349P21.11"
## [13] "COL5A3" "DAAM1" "NCAN" "ZSWIM6"
## [17] "ADGRB3" "GLTP" "TENM2" "JAZF1"
## [21] "NRG2" "ADORA1" "NAV2" "CHST11"
## [25] "LRRC8C" "CADM2" "CALCB" "LDLRAD3"
## [29] "SLC25A18" "MAML2" "FLRT2" "PLK5"
## [33] "ZNF98" "AP000318.2" "DLEU2" "PTCHD1-AS"
## [37] "AC002127.4" "MEIKIN" "LINC01252" "STX18-AS1"
## [41] "TMEM161B-AS1" "AGBL1" "RP11-358F13.1"
## [1] 15
## [1] "IQCH" "TACC2" "THSD4" "VCAN" "COL23A1"
## [6] "SYNE2" "EEF2K" "SUSD1" "CCL2" "WASF1"
## [11] "ARSB" "KLHL29" "MOB3B" "TSHZ3" "HIVEP3"
## [16] "QRICH2" "GALNT8" "PTPRE" "PLCE1" "COL6A2"
## [21] "CLVS2" "ITPRIP" "CNKSR2" "ARID5B" "SEC24D"
## [26] "RASSF3" "ORAI2" "ELAPOR2" "TMC1" "FBN1"
## [31] "FRMD3" "RCAN2" "SPACA6" "ZBTB7C" "MITF"
## [36] "NHS" "COL27A1" "RASGEF1A" "NHSL2" "LINC00685"
## [41] "L3MBTL2-AS1" "LINC00609"
## [1] 16
## [1] "CD200R1" "FAP" "LAMB4" "KLF2"
## [5] "LGR6" "AK7" "LRMDA" "KCNE4"
## [9] "GAL3ST2" "TDRD9" "ESYT3" "PPP1R36"
## [13] "METTL7B" "SLC26A5" "NOTUM" "TRDN"
## [17] "C3orf35" "LINC00862" "RP11-174G6.1" "ARL17B"
## [21] "RP5-1198O20.4" "SPRY4-AS1" "LINC01137" "KCNMB2-AS1"
## [25] "RP11-446J8.1" "LINC02315" "RP11-346L1.2" "RP11-150C16.1"
## [29] "RP11-328J6.1" "RP11-499F3.2" "CEACAM16-AS1" "KLF2-DT"
## [33] "MTRNR2L12" "RP11-711K1.8" "RP11-154H23.4" "LINC02246"
## [37] "RP11-114N1.1" "RP1-166D18.1" "RP11-465L10.14" "CTD-2201E18.6"
## [41] "RP11-103P4.1"
## [1] 17
## [1] "ID1" "SLC7A2" "SAMD4A" "APBA2"
## [5] "SEMA3C" "FOSL2" "SESN1" "PCSK5"
## [9] "GADD45B" "RNF24" "CAB39L" "KAT8"
## [13] "SPAG1" "AGFG2" "BACH2" "TFDP2"
## [17] "ID3" "FOXO3" "JUND" "SLC39A11"
## [21] "ARHGAP29" "TIAM2" "CREB5" "SEMA3D"
## [25] "SHISA5" "NFIL3" "CKB" "ZNF608"
## [29] "FOS" "JUNB" "ANO6" "MAFF"
## [33] "ZFP36L1" "DMWD" "IRS2" "EFCAB2"
## [37] "C19orf38" "AC003991.3" "RP11-507B12.1" "RP11-166M16.1"
## [41] "RP11-404C6.6"
## [1] 18
## [1] "NRXN3" "LRRC7" "STS" "IL7"
## [5] "EPM2A" "LAMA4" "PPP1R3C" "BCL2L14"
## [9] "MT2A" "CALY" "UNC79" "PDE5A"
## [13] "ABCA12" "SUMF1" "GRIK2" "HNF4G"
## [17] "JAM3" "PLD5" "PNMA3" "KIAA0825"
## [21] "NAP1L3" "EYS" "CARNMT1-AS1" "TENM3"
## [25] "AC072062.3" "SNHG31" "MIR181A1HG" "LINC00407"
## [29] "SOX2-OT" "LINC00504" "SEMA6A-AS1" "LINC02326"
## [33] "RP11-57G22.3" "RP11-1289C17.1" "RP11-335E8.3" "GAS7"
## [37] "RHOBTB1" "PXDNL" "PGM2L1" "NLGN1"
## [41] "DPYD"
## [1] 19
## [1] "SPATA17" "DNAH12" "RP1-230L10.1" "RP11-788A4.3"
## [5] "CP" "ST6GALNAC2" "PRRX1" "SOHLH2"
## [9] "HNMT" "LMNTD1" "LRGUK" "DRC1"
## [13] "CFAP251" "VWA5B1" "ABCA1" "CFAP47"
## [17] "ARMC3" "TVP23A" "TEKT1" "ATOH8"
## [21] "GSG1L" "COL24A1" "PPP1R42" "CCDC30"
## [25] "CFAP54" "TOGARAM2" "TRPV1" "WARS2-AS1"
## [29] "LINC01135" "RP11-90C4.1" "LINC01411" "LINC01088"
## [33] "CTB-35F21.1" "RP11-148E17.1" "RP11-627D16.1" "CTD-2054N24.2"
## [37] "RP11-210M15.2" "RP11-838N2.5" "RP11-35G9.5" "RP11-114N19.3"
## [41] "RP11-301F14.1" "RP11-6L16.1"
## [1] 20
## [1] "DHRS7B" "ABCC4" "FAXC" "IGFBP7" "DPP10" "ARHGAP31"
## [7] "RRP12" "PDE4A" "PDK3" "PHACTR3" "MYO9B" "COTL1"
## [13] "SYT17" "SGK1" "HIF3A" "HIP1" "RIN2" "ARHGEF4"
## [19] "BCAS3" "NFIC" "ENSA" "KCNN3" "ITPKB" "ARHGAP26"
## [25] "DOCK11" "GRIK4" "NCAM2" "C2CD2" "ABR" "DHRS3"
## [31] "ZNF704" "WNK2" "GNG4" "KCND3" "FAM222B" "SYT12"
## [37] "SH3PXD2B" "PHYHD1" "CTXN1" "APOLD1" "ANKS1B" "SRGAP1"
## [1] 21
## [1] "FAR2" "SEZ6L" "ZFR2" "GABRA4" "RGS4"
## [6] "RFC3" "BEX1" "TESPA1" "RNF165" "GULP1"
## [11] "ARHGAP18" "CCDC102B" "BTBD11" "PLEKHG4B" "SYNPR"
## [16] "NDST3" "TMEM130" "ZNF497" "KCNB2" "STAC3"
## [21] "SLIT1" "COL25A1" "IL1RAPL2" "PIWIL2" "AC011288.2"
## [26] "BAALC-AS2" "PWRN1" "KCNG1" "CDH3" "ZFY"
## [31] "TRHDE" "ARHGAP15" "KHDRBS2" "KIAA1217" "HS3ST2"
## [36] "DOCK10" "SRRM4" "KCNH5" "RIT2" "ZMAT4"
## [41] "NABP1" "VSTM2B"
## [1] 22
## [1] "PRKCQ" "F3" "DPH6" "ST6GAL2"
## [5] "SLC9B1" "OTOGL" "CYP7B1" "CASC2"
## [9] "CATSPERE" "GPR39" "DCHS2" "MALRD1"
## [13] "AC004540.5" "LINC02649" "SOX1-OT" "POT1-AS1"
## [17] "LYPLAL1-DT" "XIST" "AC079807.4" "LINC00271"
## [21] "AC007682.1" "RFX3-AS1" "UFL1-AS1" "COX10-AS1"
## [25] "RNF217-AS1" "RP11-4B14.3" "LINC02144" "RP11-268P4.5"
## [29] "LINC01182" "RP11-679C8.2" "GS1-57L11.1" "RP11-541P9.3"
## [33] "RMST" "RP11-20E24.1" "RP11-72M17.1" "LINC02328"
## [37] "PSMD7-DT" "CTC-498M16.4" "RP11-444C24.1" "RP11-221G19.1"
## [41] "RP11-96C13.1" "RP4-660H19.2" "RP11-563M4.2"
## [1] 23
## [1] "MBNL3" "GFRA1" "PDZD4" "RBFOX1" "CELF4"
## [6] "TUSC3" "PPP1R13L" "CHRNE" "TSPAN11" "PDE1A"
## [11] "B4GALT2" "NRP2" "ACVR1C" "LRRC4B" "DGKB"
## [16] "TTLL7" "SLC44A5" "RHBDL3" "ZNF385B" "DIAPH2"
## [21] "SNTG1" "CACNA1B" "CLSTN2" "EDIL3" "OXR1"
## [26] "FAT3" "FAAH2" "RBFOX3" "PDE3A" "ARPP21"
## [31] "DAB1" "ST8SIA3" "SLC25A20" "GPR137C" "ZNF804B"
## [36] "DUSP8" "KBTBD12" "PAX8-AS1" "PTPRT" "LYRM4"
## [41] "CYP1B1-AS1" "ETV5" "LINC01414"
## [1] 24
## [1] "RNF175" "KIRREL3" "MMP16" "GRIK1"
## [5] "GALNTL6" "GRM7" "RP11-170M17.1" "MSC-AS1"
## [9] "RP4-809F18.1" "RP11-640F22.1" "RP11-320L2.1" "SYT7"
## [13] "SEC14L5" "ATRNL1" "RIMS3" "SCN2A"
## [17] "CBLN2" "SLC4A10" "CDH18" "CNTN5"
## [21] "PLCL2" "SLC24A2" "CFAP161" "LRRC2"
## [25] "HTR1E" "SLC38A11" "RIMS2" "SLC8A1"
## [29] "KCNH7" "PDE2A" "CACNA1E" "LINC00632"
## [33] "TNFRSF25" "RP11-191L9.4" "XXbac-BPG55C20.7" "RP1-30E17.2"
## [37] "SHISA9" "CTC-340A15.2" "LINC01322" "PTCHD4"
## [41] "LINC02223" "RP11-624C23.1" "IQCJ-SCHIP1"
## [1] 25
## [1] "EPHA6" "TRPM3" "SCG3" "EYA1" "SLC1A2"
## [6] "EYA4" "DNAH7" "CABLES1" "CXCL14" "ACSL1"
## [11] "AXDND1" "KLHL32" "GRM3" "CNTN1" "ATP1A2"
## [16] "MCF2L2" "DGKG" "KIF3C" "CPEB3" "CCND3"
## [21] "C1orf21" "PDZRN3" "TOX2" "SYNE1" "CEP350"
## [26] "SHROOM3" "FAM171A1" "FAM13C" "PID1" "GNA14"
## [31] "AHCYL2" "CACNB2" "CACNB3" "ZFPM2" "NCKAP5"
## [36] "CNTN2" "EFNA5" "TPCN1" "ZNF785" "TOX"
## [41] "ALDH1L1-AS2"
## [1] 26
## [1] "MRC2" "TNC" "MSMO1" "IDI1"
## [5] "REEP1" "SRPX" "RIPK2" "RASD1"
## [9] "NT5DC3" "B3GAT2" "HMGCS1" "CRISPLD1"
## [13] "ADCY7" "TRIM5" "PLXNC1" "ARRDC4"
## [17] "CHST9" "ABI3BP" "FABP5" "SVEP1"
## [21] "SCG5" "GINS3" "PAPPA" "PROS1"
## [25] "INSIG1" "F5" "RP11-106M7.1" "DPP10-AS3"
## [29] "LINC01524" "AC007563.5" "RP11-239A17.1" "RP11-274G22.1"
## [33] "RP11-373E16.6" "KITLG" "FRY" "CLSTN3"
## [37] "PARP8" "SHTN1" "SMOC1" "CRYBB2"
## [41] "RP11-542F9.2"
## [1] 27
## [1] "AMPH" "BLVRB" "APBA1" "SH3D19" "GMDS" "GBE1"
## [7] "HSPH1" "ALCAM" "EXT1" "CMSS1" "BRINP2" "MRPL33"
## [13] "ITGA3" "SYN1" "EYA2" "RASAL2" "DOK5" "ARHGEF18"
## [19] "OLFM2" "DNM1" "VAV3" "CCNH" "BIN1" "SLC22A23"
## [25] "MINK1" "GABPB2" "SDK1" "DGKZ" "PTPRJ" "ADAM33"
## [31] "DOC2A" "THRB" "SPTBN4" "PKNOX2" "PLEKHA7" "PCDH7"
## [37] "REPS2" "RPS6KA3" "PARVA" "PLCG2" "DNM3"
## [1] 28
## [1] "LINC02217" "SLC26A3"
## [3] "CACNA1I" "KLHL4"
## [5] "STEAP1B" "BEST3"
## [7] "UNC13C" "ST18"
## [9] "SHROOM4" "SYTL3"
## [11] "GREM1" "SEMA3E"
## [13] "RTN4RL1" "AC023469.1"
## [15] "AC003090.1" "RP11-563D10.1"
## [17] "RP1-35C21.2" "LINC01320"
## [19] "SATB1-AS1" "RP11-147G16.1"
## [21] "RP11-154D17.1" "AC013463.2"
## [23] "RP5-827C21.2" "AC002066.1"
## [25] "RP11-384F7.1" "RP11-17A1.3"
## [27] "LINC02742" "RP11-79E3.2"
## [29] "LINC01609" "RP11-958J22.1"
## [31] "RP11-20D14.3" "RPPH1_ENSG00000259001"
## [33] "LINC00558" "AF038458.3"
## [35] "RMRP_ENSG00000269900" "SCARNA2_ENSG00000270066"
## [37] "CH507-513H4.1" "CH507-528H12.1"
## [39] "RP11-596C23.6" "RP4-799O8.1"
## [41] "AC003099.2" "RP5-1015P16.1"
## [43] "RP11-398J12.1" "RP11-4D11.1"
## [1] 29
## [1] "CDON" "ADGRL1" "TMEM38A" "GRK3"
## [5] "RIPOR2" "PADI2" "TICAM1" "RAP1GAP2"
## [9] "NKD1" "BOC" "CCDC3" "MRAS"
## [13] "FBXO27" "PTCHD1" "FAXDC2" "FZD8"
## [17] "CTD-2527I21.15" "NME9" "OSBP2" "C7orf61"
## [21] "NWD1" "TMEM184B" "PLIN5" "LINC00598"
## [25] "NRSN2-AS1" "HPN-AS1" "RP5-864K19.4" "AC104088.1"
## [29] "PDYN-AS1" "AC016745.3" "OLMALINC" "DPH6-DT"
## [33] "LINC02208" "RP11-298I3.1" "LINC02356" "RP3-414A15.10"
## [37] "RP11-507B12.2" "CASC17" "RP1-158P9.2" "AC079610.1"
## [41] "RP11-379B18.8" "RP11-26L21.1" "RP11-237N2.1"
## [1] 30
## [1] "YBX3" "NTN1" "SRBD1" "MT3" "CEMIP" "RPL18A" "RPL19"
## [8] "RPS15" "NID1" "APOE" "RPL36" "TMEM160" "CCDC59" "EMP1"
## [15] "RPLP1" "FAU" "DLC1" "ANO5" "GLRX" "A2M" "RPS27"
## [22] "LRRC3B" "ZNF48" "KCNMB2" "RPS18" "LUCAT1" "VRK2" "ICAM1"
## [29] "WFDC1" "XYLT1" "KNOP1" "KCNN1" "LOXL1" "EDA2R" "FANCC"
## [36] "FGF17" "SLC5A11" "EVA1C" "LINGO1" "SWI5" "S100A10"
## [1] 31
## [1] "PNPLA3" "SLC24A4"
## [3] "DNAAF1" "PCED1B"
## [5] "SLC4A5" "PATL2"
## [7] "LINC02615" "MAPT-AS1"
## [9] "RP5-965G21.3" "RP11-574F11.4"
## [11] "RP11-255O19.2" "DNAH5"
## [13] "ST6GAL1" "CATSPERG"
## [15] "RASL12" "AEBP1"
## [17] "CLIP2" "JHY"
## [19] "MAN1C1" "GFPT2"
## [21] "PATJ" "TTC9"
## [23] "GMPR" "DENND2A"
## [25] "ADCY8" "ST3GAL2"
## [27] "TMCO4" "C1orf87"
## [29] "DEPP1" "PRIMA1"
## [31] "SLCO3A1" "SPATA13_ENSG00000182957"
## [33] "SLC6A9" "ODAD4"
## [35] "CFI" "RP1-111D6.3"
## [37] "AC004951.6" "EPCAM-DT"
## [39] "HMGA1P4" "LINC01094"
## [41] "ZNF594-DT" "RP1-79C4.4"
## [43] "CASTOR2" "RP11-514P8.10"
## [1] 32
## [1] "UPP2" "MAMLD1" "PEX5L" "ST6GALNAC5"
## [5] "BICC1" "KIAA1328" "C4orf19" "C2CD6"
## [9] "FTH1" "RNF150" "ADRA1B" "MTSS1"
## [13] "NEGR1" "SUGCT" "TMEM132C" "TAFA1"
## [17] "WNT7B" "FIRRE" "APTR" "LCNL1"
## [21] "CRPPA" "LINC01266" "AP001628.6" "PPP1R26-AS1"
## [25] "AP000282.2" "AC008269.2" "MMADHC-DT" "RP11-154D6.1"
## [29] "PPP1R9A-AS1" "RP11-390F4.6" "DRAIC" "RP11-373N22.3"
## [33] "CTB-161M19.4" "LINC01301" "RP11-673E1.1" "RP11-317N12.1"
## [37] "RP11-134O21.1" "CTXND1" "ADGRL1-AS1" "GEMIN7-AS1"
## [41] "RP11-157E16.1" "CTC-490G23.6" "CPM"
## [1] 33
## [1] "SP140" "LINC01931" "P2RY14" "ZBTB44-DT"
## [5] "C12orf42" "FSIP2" "TSBP1" "ANKUB1"
## [9] "AC002463.3" "RP4-660H19.1" "PCDH9-AS2" "GPC5-AS2"
## [13] "PCDH9-AS4" "STARD13-AS" "RP11-475C16.2" "RP13-143G15.4"
## [17] "LINC00960" "RP11-768G7.3" "LRP4-AS1" "ANK2-AS1"
## [21] "CTD-2015H6.3" "RP11-669M16.1" "MAPK10-AS1" "RP11-517I3.1"
## [25] "ZFPM2-AS1" "RP11-116O11.1" "RP11-351A11.1" "BBOX1-AS1"
## [29] "AP000462.2" "RP11-513G19.1" "RP11-370I10.2" "RP11-39M21.1"
## [33] "PRKCA-AS1" "RP11-138H11.1" "RP11-355F16.1" "RP11-561I11.4"
## [37] "CTD-2282P23.2" "RP11-413N10.3" "RP11-576O3.1" "RP11-793H13.14"
## [41] "RP11-66G15.1" "RP11-120J1.2" "RP5-892C22.1" "RP11-168F16.1"
## [1] 34
## [1] "TENM1" "GTDC1" "TMEM108" "NDUFAF2" "GALNT10" "HPRT1" "GPR156"
## [8] "IMMP2L" "SMYD3" "PTPRN" "CAMK2B" "RIMBP2" "CTNNA2" "PLXNA2"
## [15] "TGFB2" "GLIS3" "UBE2R2" "ZMIZ1" "CLNK" "TPD52L1" "STAG1"
## [22] "MACF1" "PALLD" "SOX5" "MAPK4" "ECE2" "PAM" "ZEB1"
## [29] "CNNM2" "FOXO1" "DST" "ART3" "STX8" "BCL2" "FRMD5"
## [36] "CADM1" "EML6" "NEAT1" "CUX1"
## [1] 35
## [1] "XK" "CALCRL" "ARHGAP28" "CCDC80"
## [5] "SLC8A3" "PLCB4" "TRIM22" "FHDC1"
## [9] "LRRIQ3" "ADAMTS9" "GUCY1A1" "GFRA2"
## [13] "STK32A" "DELEC1" "SNX31" "CIITA"
## [17] "CYP4F12" "CYP4F3" "STUM" "INSYN2B"
## [21] "DIRC3" "DIRC3-AS1" "LINC02814" "AC092684.1"
## [25] "SOCS2-AS1" "NEUROG2-AS1" "RP11-364L4.3" "RP11-116N8.1"
## [29] "FRMD6-AS2" "RP11-354K4.2" "APP-DT" "RP11-323P17.2"
## [33] "LINC00836" "LINC00842" "RP11-259G3.1" "RP11-154D6.3"
## [37] "RP11-609L3.3" "RP1-20N4.2" "RP11-423B13.1" "ARHGAP6"
## [41] "NFASC" "PLPP4" "LINC02506" "LINC02251"
## [1] 36
## [1] "PON3" "MAEL" "MN1" "PAH"
## [5] "RHCE" "AC074391.1" "EPS15-AS1" "LNC-LBCS"
## [9] "LINC01185" "LINC01277" "LINC01239" "NECTIN3-AS1"
## [13] "LINC02196" "F11-AS1" "LINC00499" "MAILR"
## [17] "RP11-156K13.1" "RP11-266O8.1" "AC004158.3" "RP11-436D23.1"
## [21] "RP11-378A12.1" "CH17-174L20.1" "RP11-281A20.2" "RP11-437L7.2"
## [25] "RP11-382N13.7" "RP11-692P14.1" "RP11-624A4.2" "CTD-2297M2.1"
## [29] "LGI1" "TGIF2" "KCNJ16" "RFTN2"
## [33] "RANBP3L" "GPR176" "C2" "HPSE2"
## [37] "IQCK" "LHFPL6" "AC064875.2" "LINC00511"
## [41] "ARHGEF26-AS1" "CTD-2189E23.1" "RP11-183J19.1"
## [1] 37
## [1] "SDK2" "SYTL4" "CAP2" "WIPF1" "ENOX1"
## [6] "FAM117B" "C10orf90" "ABHD3" "NXN" "SLC43A2"
## [11] "LRRN2" "TMEM51" "SNTB1" "C1QTNF4" "CA8"
## [16] "RNLS" "ROR1" "L3MBTL3" "SAMD13" "CTC-329D1.2"
## [21] "ATP2B4" "TBC1D1" "HSD17B14" "PALM" "COBL"
## [26] "ZBTB16" "WLS" "SEM1" "FCHO1" "RFTN1"
## [31] "TNS3" "ADAMTS10" "CTDSPL" "ENOX2" "FAM107A"
## [36] "LDLRAD4" "PACS1" "GNG7" "ABAT" "HRH1"
## [41] "KIF9-AS1"
## [1] 38
## [1] "PRKAR2B" "ELAVL2" "MLIP"
## [4] "LYPD6B" "SHANK2" "CADPS"
## [7] "RGS7" "KCTD16" "CCSER1"
## [10] "DLGAP2" "RP11-410D17.2" "SYT1"
## [13] "MAP2" "CPE" "CHD5"
## [16] "PLXDC2" "DPP6" "ABCB9"
## [19] "FAM151B" "SHANK1" "ZNF653"
## [22] "ABLIM2" "GRM5" "FRMPD4"
## [25] "DLGAP1" "CSDC2" "CNTNAP2"
## [28] "PPM1E" "SAMD12" "CSMD1"
## [31] "GRIN2A" "OPCML" "RALYL"
## [34] "SYN3" "KCNQ5" "KCNIP4"
## [37] "NKAIN2" "ELAVL3" "AJAP1"
## [40] "RYR2" "MEG3" "DGCR5_ENSG00000273032"
## [1] 39
## [1] "HSD11B1" "IFI6" "GPNMB" "PLK2" "ZCCHC18"
## [6] "RAB39A" "SP140L" "PDXP" "LINC02254" "USH2A"
## [11] "NGEF" "RASGRP2" "ANGPT2" "PCDH11Y" "IGSF21"
## [16] "TNNT2" "TBX2" "ITIH5" "AIF1L" "C1QL1"
## [21] "SLC6A6" "TBX6" "CATIP" "SPATA2L" "PTMS"
## [26] "COX7A1" "VAT1L" "NXNL1" "MRGPRF" "YOD1"
## [31] "PCP4" "FAM110C" "POTEG" "FZD9" "STARD10"
## [36] "LINC01208" "HRAT92" "LINC02869" "AC067956.1" "MTRNR2L1"
## [41] "LINC01619" "PKD1L3" "RP11-93B21.2"
## [1] 40
## [1] "BCAS1" "PCSK1N" "LRRC9" "LRTM1"
## [5] "HHIP" "CLMP" "NRG4" "SEPTIN1"
## [9] "CYP4X1" "AC026188.1" "LINC01117" "AC105461.1"
## [13] "Z83001.1" "CCDC26" "RP11-141A19.1" "IPO9-AS1"
## [17] "LINC01725" "LINC01877" "RP11-446H18.5" "RP11-114J13.1"
## [21] "VCAN-AS1" "RP11-348J24.1" "RP11-711G10.1" "STPG2-AS1"
## [25] "RP11-586K2.1" "RP11-649G15.2" "AB015752.3" "RP11-624D11.2"
## [29] "LINC02389" "RP11-867G2.8" "RP11-315E17.1" "RP11-104E19.1"
## [33] "LINC01579" "PTCSC3" "RP11-184D12.1" "TSIX"
## [37] "LINC02664" "RP11-80I3.1" "SLC7A14-AS1" "CTC-428H11.2"
## [41] "RP5-847G17.1" "CTD-2172F7.1" "RP11-875G18.1" "CCK"
## [45] "AC092155.4"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_17"
## [1] "ID1" "SLC7A2" "SAMD4A" "APBA2"
## [5] "SEMA3C" "FOSL2" "SESN1" "PCSK5"
## [9] "GADD45B" "RNF24" "CAB39L" "KAT8"
## [13] "SPAG1" "AGFG2" "BACH2" "TFDP2"
## [17] "ID3" "FOXO3" "JUND" "SLC39A11"
## [21] "ARHGAP29" "TIAM2" "CREB5" "SEMA3D"
## [25] "SHISA5" "NFIL3" "CKB" "ZNF608"
## [29] "FOS" "JUNB" "ANO6" "MAFF"
## [33] "ZFP36L1" "DMWD" "IRS2" "EFCAB2"
## [37] "C19orf38" "AC003991.3" "RP11-507B12.1" "RP11-166M16.1"
## [41] "RP11-404C6.6"
## $reactome
## category
## 604 ngf stimulated transcription
## 947 signaling by ntrks
## 626 nuclear events kinase and transcription factor activation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 604 1.470466e-06 1.0000000 5 10
## 947 5.745032e-06 0.9999997 7 25
## 626 1.519618e-05 0.9999995 5 13
## FDR
## 604 0.001651333
## 947 0.003225835
## 626 0.005688436
##
## [1] "set_19"
## [1] "SPATA17" "DNAH12" "RP1-230L10.1" "RP11-788A4.3"
## [5] "CP" "ST6GALNAC2" "PRRX1" "SOHLH2"
## [9] "HNMT" "LMNTD1" "LRGUK" "DRC1"
## [13] "CFAP251" "VWA5B1" "ABCA1" "CFAP47"
## [17] "ARMC3" "TVP23A" "TEKT1" "ATOH8"
## [21] "GSG1L" "COL24A1" "PPP1R42" "CCDC30"
## [25] "CFAP54" "TOGARAM2" "TRPV1" "WARS2-AS1"
## [29] "LINC01135" "RP11-90C4.1" "LINC01411" "LINC01088"
## [33] "CTB-35F21.1" "RP11-148E17.1" "RP11-627D16.1" "CTD-2054N24.2"
## [37] "RP11-210M15.2" "RP11-838N2.5" "RP11-35G9.5" "RP11-114N19.3"
## [41] "RP11-301F14.1" "RP11-6L16.1"
## $go_bp
## category over_represented_pvalue
## 560 cilium or flagellum dependent cell motility 9.377027e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 560 0.9999997 5 19 0.04210285
##
## [1] "set_20"
## [1] "DHRS7B" "ABCC4" "FAXC" "IGFBP7" "DPP10" "ARHGAP31"
## [7] "RRP12" "PDE4A" "PDK3" "PHACTR3" "MYO9B" "COTL1"
## [13] "SYT17" "SGK1" "HIF3A" "HIP1" "RIN2" "ARHGEF4"
## [19] "BCAS3" "NFIC" "ENSA" "KCNN3" "ITPKB" "ARHGAP26"
## [25] "DOCK11" "GRIK4" "NCAM2" "C2CD2" "ABR" "DHRS3"
## [31] "ZNF704" "WNK2" "GNG4" "KCND3" "FAM222B" "SYT12"
## [37] "SH3PXD2B" "PHYHD1" "CTXN1" "APOLD1" "ANKS1B" "SRGAP1"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 116 cdc42 gtpase cycle 3.585973e-05 0.9999973
## 739 rac1 gtpase cycle 4.742297e-05 0.9999962
## numDEInCat numInCat FDR
## 116 7 23 0.026628
## 739 7 26 0.026628
##
## [1] "set_24"
## [1] "RNF175" "KIRREL3" "MMP16" "GRIK1"
## [5] "GALNTL6" "GRM7" "RP11-170M17.1" "MSC-AS1"
## [9] "RP4-809F18.1" "RP11-640F22.1" "RP11-320L2.1" "SYT7"
## [13] "SEC14L5" "ATRNL1" "RIMS3" "SCN2A"
## [17] "CBLN2" "SLC4A10" "CDH18" "CNTN5"
## [21] "PLCL2" "SLC24A2" "CFAP161" "LRRC2"
## [25] "HTR1E" "SLC38A11" "RIMS2" "SLC8A1"
## [29] "KCNH7" "PDE2A" "CACNA1E" "LINC00632"
## [33] "TNFRSF25" "RP11-191L9.4" "XXbac-BPG55C20.7" "RP1-30E17.2"
## [37] "SHISA9" "CTC-340A15.2" "LINC01322" "PTCHD4"
## [41] "LINC02223" "RP11-624C23.1" "IQCJ-SCHIP1"
## $go_bp
## category over_represented_pvalue
## 3799 regulation of trans synaptic signaling 9.196575e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 3799 0.999999 10 97 0.04129262
##
## [1] "set_26"
## [1] "MRC2" "TNC" "MSMO1" "IDI1"
## [5] "REEP1" "SRPX" "RIPK2" "RASD1"
## [9] "NT5DC3" "B3GAT2" "HMGCS1" "CRISPLD1"
## [13] "ADCY7" "TRIM5" "PLXNC1" "ARRDC4"
## [17] "CHST9" "ABI3BP" "FABP5" "SVEP1"
## [21] "SCG5" "GINS3" "PAPPA" "PROS1"
## [25] "INSIG1" "F5" "RP11-106M7.1" "DPP10-AS3"
## [29] "LINC01524" "AC007563.5" "RP11-239A17.1" "RP11-274G22.1"
## [33] "RP11-373E16.6" "KITLG" "FRY" "CLSTN3"
## [37] "PARP8" "SHTN1" "SMOC1" "CRYBB2"
## [41] "RP11-542F9.2"
## $go_bp
## category over_represented_pvalue
## 4220 sterol biosynthetic process 5.056125e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4220 1 4 6 0.022702
##
## [1] "set_30"
## [1] "YBX3" "NTN1" "SRBD1" "MT3" "CEMIP" "RPL18A" "RPL19"
## [8] "RPS15" "NID1" "APOE" "RPL36" "TMEM160" "CCDC59" "EMP1"
## [15] "RPLP1" "FAU" "DLC1" "ANO5" "GLRX" "A2M" "RPS27"
## [22] "LRRC3B" "ZNF48" "KCNMB2" "RPS18" "LUCAT1" "VRK2" "ICAM1"
## [29] "WFDC1" "XYLT1" "KNOP1" "KCNN1" "LOXL1" "EDA2R" "FANCC"
## [36] "FGF17" "SLC5A11" "EVA1C" "LINGO1" "SWI5" "S100A10"
## $reactome
## category
## 287 eukaryotic translation elongation
## 288 eukaryotic translation initiation
## 610 nonsense mediated decay nmd
## 810 response of eif2ak4 gcn2 to amino acid deficiency
## 878 selenoamino acid metabolism
## 856 rrna processing
## 975 srp dependent cotranslational protein targeting to membrane
## 429 influenza infection
## 1078 translation
## 762 regulation of expression of slits and robos
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 287 1.136754e-11 1 8 9
## 288 1.136754e-11 1 8 9
## 610 1.136754e-11 1 8 9
## 810 6.292460e-11 1 8 10
## 878 7.081812e-11 1 8 10
## 856 7.229398e-11 1 8 10
## 975 2.493638e-10 1 8 11
## 429 2.510579e-10 1 8 11
## 1078 1.935771e-09 1 8 13
## 762 2.057827e-09 1 8 13
## FDR
## 287 4.255248e-09
## 288 4.255248e-09
## 610 4.255248e-09
## 810 1.353102e-08
## 878 1.353102e-08
## 856 1.353102e-08
## 975 3.524226e-08
## 429 3.524226e-08
## 1078 2.310939e-07
## 762 2.310939e-07
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation 0 1
## numDEInCat numInCat FDR
## 618 9 12 0
##
## [1] "set_38"
## [1] "PRKAR2B" "ELAVL2" "MLIP"
## [4] "LYPD6B" "SHANK2" "CADPS"
## [7] "RGS7" "KCTD16" "CCSER1"
## [10] "DLGAP2" "RP11-410D17.2" "SYT1"
## [13] "MAP2" "CPE" "CHD5"
## [16] "PLXDC2" "DPP6" "ABCB9"
## [19] "FAM151B" "SHANK1" "ZNF653"
## [22] "ABLIM2" "GRM5" "FRMPD4"
## [25] "DLGAP1" "CSDC2" "CNTNAP2"
## [28] "PPM1E" "SAMD12" "CSMD1"
## [31] "GRIN2A" "OPCML" "RALYL"
## [34] "SYN3" "KCNQ5" "KCNIP4"
## [37] "NKAIN2" "ELAVL3" "AJAP1"
## [40] "RYR2" "MEG3" "DGCR5_ENSG00000273032"
## $reactome
## category over_represented_pvalue
## 595 neurexins and neuroligins 1.081398e-07
## 596 neuronal system 1.284096e-07
## 725 protein protein interactions at synapses 1.098913e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 595 1 7 18 7.210198e-05
## 596 1 11 72 7.210198e-05
## 725 1 7 25 4.113598e-04
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955042 478.3 16112782 860.6 NA 15574709 831.8
## Vcells 16666262 127.2 31262822 238.6 65536 31262822 238.6
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0